Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine

Wang, Ligang; Xu, Lingyang; Liu, Xin; Zhang, Tiantian; Li, Na; Hay, El Hamidi; Zhang, Yuebo; Yan, H.J.; Zhao, Kelei; Liu, George E.; Zhang, Longchao; Wang, Lixian

doi:10.1038/srep12535

Cited by 33 publications

(30 citation statements)

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“…A CNV involving the AKR1C gene is considered possibly responsible for testicular androgen synthesis and sexual development in horse [ 3 ]. The DNA dosage and EST expression of CNVs overlapping with the Ntn1 gene may influence meat quality in pigs [ 20 ]. In bovid species, several important genes related to clear phenotypic changes and breed differences have been modified by CNVs: the copy number variations of the HSFY and ZNF280BY genes are associated with male reproductive traits in Holstein bulls [ 21 ]; PLA2G2D located in a CNV region is associated with aspects of body size in Chinese bulls such as heart girth and hucklebone width [ 22 ]; hereditary myopathy of diaphragmatic muscles in Holstein-Friesian cattle has been linked to deletion of the HSPA1B gene [ 23 ]; and the APOL3 gene involved in lipid transport is highly duplicated in beef breeds [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide patterns of copy number variation in the Chinese yak genome

Zhang

Wang

et al. 2016

BMC Genomics

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BackgroundCopy number variation (CNV) represents an important source of genetic divergence that can produce drastic phenotypic differences and may therefore be subject to selection during domestication and environmental adaptation. To investigate the evolutionary dynamics of CNV in the yak genome, we used a read depth approach to detect CNV based on genome resequencing data from 14 wild and 65 domestic yaks and determined CNV regions related to domestication and adaptations to high-altitude.ResultsWe identified 2,634 CNV regions (CNVRs) comprising a total of 153 megabases (5.7 % of the yak genome) and 3,879 overlapping annotated genes. Comparison between domestic and wild yak populations identified 121 potentially selected CNVRs, harboring genes related to neuronal development, reproduction, nutrition and energy metabolism. In addition, we found 85 CNVRs that are significantly different between domestic yak living in high- and low-altitude areas, including three genes related to hypoxia response and six related to immune defense. This analysis shows that genic CNVs may play an important role in phenotypic changes during yak domestication and adaptation to life at high-altitude.ConclusionsWe present the first refined CNV map for yak along with comprehensive genomic analysis of yak CNV. Our results provide new insights into the genetic basis of yak domestication and adaptation to living in a high-altitude environment, as well as a valuable genetic resource that will facilitate future CNV association studies of important traits in yak and other bovid species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2702-6) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genome-wide patterns of copy number variation in the Chinese yak genome

Zhang

Wang

et al. 2016

BMC Genomics

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“…In plants, a SV affecting three genes was linked to pathogen resistance in soybean [20] and a gene duplication was shown to cause higher grain yield in rice [21]. Studying CNV at the genome level can even reveal evolutionary footprints, as within the primate lineage [22], which implies that inherited CNVs are subject to the same evolutionary forces as all other DNA polymorphisms.…”

Section: Introductionmentioning

confidence: 99%

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation

2017

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BackgroundCopy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid.ResultsWe discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs.ConclusionsThe approach we developed is of particular interest in non-model species lacking a reference genome. Our findings point to a role for CNVs in adaptation. Their reduced abundance in the hybrid may limit genetic variability and evolvability of hybrids. We propose that CNVs make a qualitatively distinct contribution to adaptation which could be important for short term change.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3458-8) contains supplementary material, which is available to authorized users.

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“…Another possibility is the effect of the copy number variant (CNV), which could not be accounted for in the SNP array. Recent studies have reported the association between CNV and economically important traits in pigs [ 26 , 27 ]. In real data analysis of haplotype-based GWAS of color-sidedness traits in a cattle population, Zhang et al [ 18 ] reported that ancestral haplotypes presented high LD with CNVs that had been previously reported by Durkin et al [ 28 ]; however, the same region was not significant following analysis of SNP-based GWAS.…”

Section: Discussionmentioning

confidence: 99%

SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

et al. 2016

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BackgroundThe aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, and to detect novel candidate genes affecting economically important traits in a purebred Duroc population comprising seven-generation pedigree. First, we performed a simulation analysis using real genotype data of this population to compare the power (based on the null hypothesis) of the two methods. We then performed GWAS using both methods and real phenotype data comprising 52 traits, which included growth, carcass, and meat quality traits.ResultsIn total, 836 animals were genotyped using the Illumina PorcineSNP60 BeadChip and 14 customized SNPs from regions of known candidate genes related to the traits of interest. The power of SNP-based GWAS was greater than that of haplotype-based GWAS in a simulation analysis. In real data analysis, a larger number of significant regions was obtained by SNP-based GWAS than by haplotype-based GWAS. For SNP-based GWAS, 23 genome-wide significant SNP regions were detected for 17 traits, and 120 genome-wide suggestive SNP regions were detected for 27 traits. For haplotype-based GWAS, 6 genome-wide significant SNP regions were detected for four traits, and 11 genome-wide suggestive SNP regions were detected for eight traits. All genome-wide significant SNP regions detected by haplotype-based GWAS were located in regions also detected by SNP-based GWAS. Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35–39 Mb, 41–42 Mb, and 103 Mb. The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths. Mapped QTL regions contain some candidate genes involved in skeletal formation (FUBP3; far upstream element binding protein 3) and fat deposition (METTL3; methyltransferase like 3).ConclusionOur results show that a multigenerational pig population is useful for detecting QTL, which are typically segregated in a purebred population. In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0368-3) contains supplementary material, which is available to authorized users.

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Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine

Cited by 33 publications

References 62 publications

Genome-wide patterns of copy number variation in the Chinese yak genome

Genome-wide patterns of copy number variation in the Chinese yak genome

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation

SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

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